Recycler: an algorithm for detecting plasmids from de novo assembly graphs
Sign Up to like & getrecommendations! Published in 2017 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btw651
Abstract: Motivation: Plasmids and other mobile elements are central contributors to microbial evolution and genome innovation. Recently, they have been found to have important roles in antibiotic resistance and in affecting production of metabolites used in… read more here.
Keywords: detecting plasmids; assembly graphs; algorithm detecting; recycler algorithm ... See more keywords
Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity
Sign Up to like & getrecommendations! Published in 2020 at "Genome Biology"
DOI: 10.1186/s13059-020-02066-4
Abstract: Genomes computationally inferred from large metagenomic data sets are often incomplete and may be missing functionally important content and strain variation. We introduce an information retrieval system for large metagenomic data sets that exploits the… read more here.
Keywords: large metagenome; assembly graphs; neighborhoods large; exploring neighborhoods ... See more keywords
Integrating Hi-C links with assembly graphs for chromosome-scale assembly
Sign Up to like & getrecommendations! Published in 2019 at "PLoS Computational Biology"
DOI: 10.1371/journal.pcbi.1007273
Abstract: Long-read sequencing and novel long-range assays have revolutionized de novo genome assembly by automating the reconstruction of reference-quality genomes. In particular, Hi-C sequencing is becoming an economical method for generating chromosome-scale scaffolds. Despite its increasing… read more here.
Keywords: chromosome scale; assembly graphs; integrating links; assembly ... See more keywords